SMTL ID : 9dpp.1

BMP-9 Wild-Type Dimer in Acidic pH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: P.81, I.82, S.83, Y.97, H.98, Y.99 Ligands: NA.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.82, A:S.83, A:S.83, A:H.98 GOL.2: 10 residues within 4Å: Chain A: C.37, C.73, C.74, V.75, P.76 Chain B: Q.58, K.71, A.72, C.73, R.110 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:C.37, A:C.74, B:Q.58, B:Q.58 Water bridges: A:C.37 GOL.17: 7 residues within 4Å: Chain B: P.81, I.82, S.83, Y.97, H.98, Y.99 Ligands: NA.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.82, B:S.83, B:S.83, B:H.98 GOL.18: 10 residues within 4Å: Chain A: Q.58, K.71, A.72, C.73, R.110 Chain B: C.37, C.73, C.74, V.75, P.76 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:C.37, B:C.74, A:Q.58, A:Q.58 Water bridges: B:C.37

18 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: K.96, Y.97, H.98 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: K.96, H.98, Y.99, E.100 Chain B: K.53 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: L.79 Chain B: T.52 Ligands: NA.12 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: T.52, K.53 Chain B: G.101 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: F.43, P.44, L.45 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: T.50, T.52, R.110 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: H.62, P.66 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: G.5, H.7, P.44 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: Y.97, H.98 Ligands: NA.16 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: K.96, Y.97, H.98 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain A: K.53 Chain B: K.96, H.98, Y.99, E.100 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain A: T.52 Chain B: L.79 Ligands: NA.28 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain A: G.101 Chain B: T.52, K.53 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain B: F.43, P.44, L.45 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain B: T.50, T.52, R.110 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: H.62, P.66 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: G.5, H.7, P.44 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: Y.97, H.98 Ligands: NA.32 Ligand excluded by PLIP

10 x NA: SODIUM ION(Non-functional Binders)

NA.12: 6 residues within 4Å: Chain A: P.76, T.77, L.79 Chain B: T.52, R.110 Ligands: CL.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.76 NA.13: 4 residues within 4Å: Chain A: K.78, L.79, S.80, P.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.100 Water bridges: A:E.100 NA.14: 3 residues within 4Å: Chain A: G.39, C.73, C.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.39, A:C.74 NA.15: 4 residues within 4Å: Chain A: F.65, P.66, T.67, K.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.67, A:T.67 NA.16: 2 residues within 4Å: Ligands: GOL.1, CL.11 No protein-ligand interaction detected (PLIP) NA.28: 6 residues within 4Å: Chain A: T.52, R.110 Chain B: P.76, T.77, L.79 Ligands: CL.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.76 NA.29: 4 residues within 4Å: Chain B: K.78, L.79, S.80, P.81 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.100 NA.30: 3 residues within 4Å: Chain B: G.39, C.73, C.74 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.74 Water bridges: B:G.39 NA.31: 4 residues within 4Å: Chain B: F.65, P.66, T.67, K.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.67, B:T.67, B:T.67 NA.32: 2 residues within 4Å: Ligands: GOL.17, CL.27 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schwartze, T.A. et al., Molecular Basis of Interchain Disulfide Bond Formation in BMP-9 and BMP-10. J.Mol.Biol. (2025)

Release Date

2025-03-05

Peptides

Growth/differentiation factor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Growth/differentiation factor 2

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